Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction

Molecular dynamics simulation of Escherichia coli trp-repressor/operator complex was performed to elucidate protein–DNA interactions in solution for 800 ps on special-purpose computer MD-GRAPE. The Ewald summation method was employed to treat the electrostatic interaction without cutoff. DNA kept stable conformation in comparison with the result of the conventional cutoff method. Thus, the trajectories obtained were used to analyze the protein–DNA interaction and to understand the role of dynamics of water molecules forming sequence specific recognition interface. The dynamical cross-correlation map showed a significant positive correlation between the helix-turn-helix DNA-binding motifs and the major grooves of operator DNA. The extensive contact surface was stable during the simulation. Most of the contacts consisted of direct interactions between phosphates of DNA and the protein, but several water-mediated polar contacts were also observed. These water-mediated interactions, which were also seen in the crystal structure (Z. Otwinowski, et al., Nature, 335 (1998) 321) emerged spontaneously from the randomized initial configuration of the solvent. This result suggests the importance of the water-mediated interaction in specific recognition of DNA by the trp-repressor, consistent with X-ray structural information.     

Soluble polyphenol

Soluble polyphenol was synthesized for the first time by enzymatic oxidative polymerization of phenol using peroxidase and hydrogen peroxide as catalyst and oxidizing agent, respectively. A mixed solvent of alcohol and buffer improved the polymer solubility toward N,N-dimethylformamide (DMF). The resulting polymer was composed of a mixture of phenylene and oxyphenylene units. Changing the solvent composition could control the molecular weight and regioselectivity of the polymer. The polymer was found to possess relatively high thermal stability.     

Universal Single-Mode Lasing in Fully Chaotic Billiard Lasers

By numerical simulations and experiments of fully chaotic billiard lasers, we show that single-mode lasing states are stable, whereas multi-mode lasing states are unstable when the size of the billiard is much larger than the wavelength and the external pumping power is sufficiently large. On the other hand, for integrable billiard lasers, it is shown that multi-mode lasing states are stable, whereas single-mode lasing states are unstable. These phenomena arise from the combination of two different nonlinear effects of mode-interaction due to the active lasing medium and deformation of the billiard shape. Investigations of billiard lasers with various shapes revealed that single-mode lasing is a universal phenomenon for fully chaotic billiard lasers.     

The core of an economy with a common pool resource: A partition function form approach

In this paper we consider a model of an economy with a common pool resource. Under decreasing returns to scale, it is well-known that no Nash equilibrium attains Pareto efficiency. We examine whether it is possible to achieve Pareto efficiency and avoid the tragedy of the commons through cooperation among players. For that purpose, we use the notion of a game in partition function form. Whether or not the core exists depends crucially on the expectations of each coalition regarding the coalition formation of the outsiders. If each coalition has pessimistic expectations, then the core always exists, while if it has optimistic expectations, the core may be empty. Received: January 1998/Final version: November 1998     

Grain-boundary faceting at a = 3, [110]/{112} grain boundary in a cubic zirconia bicrystal

The atomic structure of a = 3, [110]/{112} grain boundary in a yttria-stabilized cubic zirconia bicrystal has been investigated by high-resolution transmission electron microscopy (HRTEM). It was found that the grain boundary migrated to form periodic facets, although the bicrystal was initially joined so as to have the symmetric boundary plane of {112}. The faceted boundary planes were indexed as {111}/{115}. The structure of the {111}/{115} grain boundary was composed of an alternate array of two types of structure unit: {112}- and {111}-type structure units. HRTEM observations combined with lattice statics calculations verified that both crystals were relatively shifted by (α/4)[110] along the rotation axis to form a stable grain-boundary structure. A weak-beam dark-field image revealed that there was a periodic array of dislocations along the grain boundary. The grain-boundary dislocations were considered to be introduced by the slight misorientation from the perfect = 3 orientation. The fact that the periodicity of the facets corresponded to that of the grain-boundary dislocations must indicate that the introduction of the grain-boundary dislocations is closely related to the periodicity of the facets. An atomic flipping model has been proposed for the facet growth from the initial = 3, {112} grain boundary.